1. An Introduction to Scratchpads: Making your data work for you Laurence Livermore Natural History Museum, London l.livermore@nhm.ac.uk Joinville, Brazil November, 2012

2. What are Scratchpads? Hosted websites for biodiversity data Virtual research & publication platform Completely open access & open source Modular & flexible 2 of

3. What Scratchpads are not! A single biodiversity database Restricted thematically, geographically or taxonomically A tool just for taxonomists 3 of

4. How are Scratchpads funded? 4 of 2007 2011 2014 ViBRANT Virtual Biodiversity Research &

5. Examples of usage: 5 of Taxa (Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) Projects Conservation RegionsSocieties

6. Who uses Scratchpads? Total Sites: 400+ Total Users: 7,000+ Active Users: 5,500+ (273 w / 759 m) Content: 430,000+ Sites Users ViBRANT SP 2 Professional scientists Amateur naturalists Citizen scientists Individuals, groups & societies

7. eMonocot Scratchpads 15 sites and growing 40+ international users Scratchpads / eMonocot Portal now active! Site list: http://about.e-monocot.org/list-emonocot-scratchpadshttp://about.e-monocot.org/list-emonocot-scratchpads

8. Why Scratchpads? Science is global It needs global standards Global workflows Cooperation of large institutes and organisations 8 of

9. Why Scratchpads? Science is carried out “locally” By local scientists Involvement with local infrastructures Funded locally 9 of

10. Why Scratchpads? This leads to: A complex, fragmented & hard to navigate landscape Dispersed data sources Difficulties for collecting information for research 10 of

11. Why should we change? The problems with traditional published data: Most descriptions are under copyright (~1923) Limited Open Access and accessibility No mechanism for updates & corrections Little or no data integration (except citations) No mechanism for community engagement 11 of

12. Why should we change? This results in: Vast amounts of unpublished taxonomic “knowledge” The knowledge that is published cannot be mobilised Low scientific impact (but long half-life) 12 of

13. The Scratchpad Concept A Scratchpad is a website that holds data for you and your community 13 of Your data External data & services

14. What can Scratchpads do? Taxon pages (generated from tagged content) Distribution maps (from specimens and TDWG regional distributions - Brummitt, 2001) Specimen records Character matrixes 14 of

15. Example Taxon Page

16. Example regional distribution

17. What can Scratchpads do? Bibliography management Images, video and sound (bulk import) Excel spreadsheet import

18. Example Literature

19. What can Scratchpads do? Tabular data editing Custom content User management Custom webforms Analytics

21. What can Scratchpads do? Darwin Core Archive export (links to eMonocot Portal and EOL) EOL data import (taxonomy, species information) GBIF Map integration

22. Getting data in and out of Scratchpads

23. What new features are coming soon? Matrix-based keys using the character project Publication tool - submit manuscripts through your site via Phytokeys or the new Biodiversity Data Journal Checklists, multiple language support and more!

24. Testing screenshots of the publishing tool ID Key preview Multi-figure platesPlate layout ID Key builder Manuscript preview

25. Help & Support In-site Support -One click help within your site Wiki -Training manuals, videos & glossary Training Courses (12 in 2012) -UK (6), Sweden, (2) Greece (1), Bulgaria (1), South Africa (1), Brazil (1) Ambassadors Programme -Enthusiastic experienced users -Local support Embedded Issues Queue -Bug reports -Feature requests Sandbox Site -http://sandbox.scratchpad.euhttp://sandbox.scratchpad.eu http://scratchpad.eu/help

26. Scratchpad technical development -Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton & Katherine Boulton Scratchpad outreach -Irina Brake & Dimitris Koureas E-Monocot -Paul Wilkin & the Kew team, Charles Godfray & the Oxford team ViBRANT -Vince Smith, Dave Roberts & Lucy Reeve Our 7,000+ users Acknowledgements

28. Security & Backups Nightly backups of database and files Off-site tape backup Whole-site archives available upon request Berlin mirror

29. Technical Infrastructure LAMP (standard open source setup) Multiple virtual servers (scaleable) Aegir hosting system (multisite management)